Dataset Card for BEIR Benchmark

trec-covid is one of the datasets from the Bio-Medical Retrieval task within BEIR, measuring scientific article retrieval for a given query on COVID-19.

  Dataset Summary

BEIR is a heterogeneous benchmark built from 18 diverse datasets representing 9 information retrieval tasks.

Fact-checking: FEVER, Climate-FEVER, SciFact Question-Answering: NQ, HotpotQA, FiQA-2018 Bio-Medical IR: TREC-COVID, BioASQ, NFCorpus News Retrieval: TREC-NEWS… See the full description on the dataset page: https://huggingface.co/datasets/BeIR/trec-covid.

Content:

"Our World in Data" which in collaboration with The University of Oxford have developed a reliable repository of datasets about dozens of topics focusing on those big problems which affect the world. This is why since the beginning of COVID-19 outbreak several researchers have been collecting data from every country in the world about multiple indicators which can make us take better decisions, what is more amazing is the fact that this dataset offered is updated every day for all countries allowing people to keep track of it. In the following link you can find fascinating charts about the pandemic and obviously the World COVID-19 dataset (up to date) containing over 60 features which you can download for free:

https://ourworldindata.org/covid-vaccinations

Important to consider:

I will be updating this dataset every week according to the published data by the organization, if you found this dataset or the link given useful I would really appreciate your upvote!

Acknowledgements and Citation

Mathieu, E., Ritchie, H., Ortiz-Ospina, E. et al. A global database of COVID-19 vaccinations. Nat Hum Behav (2021)

Note: Reporting of new COVID-19 Case Surveillance data will be discontinued July 1, 2024, to align with the process of removing SARS-CoV-2 infections (COVID-19 cases) from the list of nationally notifiable diseases. Although these data will continue to be publicly available, the dataset will no longer be updated.

Authorizations to collect certain public health data expired at the end of the U.S. public health emergency declaration on May 11, 2023. The following jurisdictions discontinued COVID-19 case notifications to CDC: Iowa (11/8/21), Kansas (5/12/23), Kentucky (1/1/24), Louisiana (10/31/23), New Hampshire (5/23/23), and Oklahoma (5/2/23). Please note that these jurisdictions will not routinely send new case data after the dates indicated. As of 7/13/23, case notifications from Oregon will only include pediatric cases resulting in death.

This case surveillance publicly available dataset has 33 elements for all COVID-19 cases shared with CDC and includes demographics, geography (county and state of residence), any exposure history, disease severity indicators and outcomes, and presence of any underlying medical conditions and risk behaviors. This dataset requires a registration process and a data use agreement.

CDC has three COVID-19 case surveillance datasets:

• COVID-19 Case Surveillance Public Use Data with Geography: Public use, patient-level dataset with clinical data (including symptoms), demographics, and county and state of residence. (19 data elements)
• COVID-19 Case Surveillance Public Use Data: Public use, patient-level dataset with clinical and symptom data and demographics, with no geographic data. (12 data elements)
• COVID-19 Case Surveillance Restricted Access Detailed Data: Restricted access, patient-level dataset with clinical and symptom data, demographics, and state and county of residence. Access requires a registration process and a data use agreement. (33 data elements)

Requesting Access to the COVID-19 Case Surveillance Restricted Access Detailed Data Please review the following documents to determine your interest in accessing the COVID-19 Case Surveillance Restricted Access Detailed Data file: 1) CDC COVID-19 Case Surveillance Restricted Access Detailed Data: Summary, Guidance, Limitations Information, and Restricted Access Data Use Agreement Information 2) Data Dictionary for the COVID-19 Case Surveillance Restricted Access Detailed Data The next step is to complete the Registration Information and Data Use Restrictions Agreement (RIDURA). Once complete, CDC will review your agreement. After access is granted, Ask SRRG (eocevent394@cdc.gov) will email you information about how to access the data through GitHub. If you have questions about obtaining access, email eocevent394@cdc.gov.

Overview

The COVID-19 case surveillance database includes individual-level data reported to U.S. states and autonomous reporting entities, including New York City and the District of Columbia (D.C.), as well as U.S. territories and affiliates. On April 5, 2020, COVID-19 was added to the Nationally Notifiable Condition List and classified as “immediately notifiable, urgent (within 24 hours)” by a Council of State and Territorial Epidemiologists (CSTE) Interim Position Statement (Interim-20-ID-01). CSTE updated the position statement on August 5, 2020, to clarify the interpretation of antigen detection tests and serologic test results within the case classification (Interim-20-ID-02). The statement also recommended that all states and territories enact laws to make COVID-19 reportable in their jurisdiction, and that jurisdictions conducting surveillance should submit case notifications to CDC. COVID-19 case surveillance data are collected by jurisdictions and reported voluntarily to CDC.

COVID-19 case surveillance data are collected by jurisdictions and are shared voluntarily with CDC. For more information, visit: https://www.cdc.gov/coronavirus/2019-ncov/covid-data/about-us-cases-deaths.html.

The deidentified data in the restricted access dataset include demographic characteristics, state and county of residence, any exposure history, disease severity indicators and outcomes, clinical data, laboratory diagnostic test results, and comorbidities.

All data elements can be found on the COVID-19 case report form located at www.cdc.gov/coronavirus/2019-ncov/downloads/pui-form.pdf.

COVID-19 case reports have been routinely submitted using standardized case reporting forms.

On April 5, 2020, CSTE released an Interim Position Statement with national surveillance case definitions for COVID-19 included. Current versions of these case definitions are available here: https://ndc.services.cdc.gov/case-definitions/coronavirus-disease-2019-2021/.

CSTE updated the position statement on August 5, 2020, to clarify the interpretation of antigen detection tests and serologic test results within the case classification. All cases reported on or after were requested to be shared by public health departments to CDC using the standardized case definitions for lab-confirmed or probable cases.

On May 5, 2020, the standardized case reporting form was revised. Case reporting using this new form is ongoing among U.S. states and territories.

Data are Considered Provisional

• The COVID-19 case surveillance data are dynamic; case reports can be modified at any time by the jurisdictions sharing COVID-19 data with CDC. CDC may update prior cases shared with CDC based on any updated information from jurisdictions. For instance, as new information is gathered about previously reported cases, health departments provide updated data to CDC. As more information and data become available, analyses might find changes in surveillance data and trends during a previously reported time window. Data may also be shared late with CDC due to the volume of COVID-19 cases.
• Annual finalized data: To create the final NNDSS data used in the annual tables, CDC works carefully with the reporting jurisdictions to reconcile the data received during the year until each state or territorial epidemiologist confirms that the data from their area are correct.

Access Addressing Gaps in Public Health Reporting of Race and Ethnicity for COVID-19, a report from the Council of State and Territorial Epidemiologists, to better understand the challenges in completing race and ethnicity data for COVID-19 and recommendations for improvement.

Data Limitations

To learn more about the limitations in using case surveillance data, visit FAQ: COVID-19 Data and Surveillance.

Data Quality Assurance Procedures

CDC’s Case Surveillance Section routinely performs data quality assurance procedures (i.e., ongoing corrections and logic checks to address data errors). To date, the following data cleaning steps have been implemented:

• Questions that have been left unanswered (blank) on the case report form are reclassified to a Missing value, if applicable to the question. For example, in the question "Was the individual hospitalized?" where the possible answer choices include "Yes," "No," or "Unknown," the blank value is recoded to "Missing" because the case report form did not include a response to the question.
• Logic checks are performed for date data. If an illogical date has been provided, CDC reviews the data with the reporting jurisdiction. For example, if a symptom onset date in the future is reported to CDC, this value is set to null until the reporting jurisdiction updates the date appropriately.
• Additional data quality processing to recode free text data is ongoing. Data on symptoms, race, ethnicity, and healthcare worker status have been prioritized.

Data Suppression

To prevent release of data that could be used to identify people, data cells are suppressed for low frequency (<11 COVID-19 case records with a given values). Suppression includes low frequency combinations of case month, geographic characteristics (county and state of residence), and demographic characteristics (sex, age group, race, and ethnicity). Suppressed values are re-coded to the NA answer option; records with data suppression are never removed.

Additional COVID-19 Data

COVID-19 data are available to the public as summary or aggregate count files, including total counts of cases and deaths by state and by county. These and other COVID-19 data are available from multiple public locations:

2020

A centralized repository of up-to-date and curated datasets on or related to the spread and characteristics of the novel corona virus (SARS-CoV-2) and its associated illness, COVID-19. Globally, there are several efforts underway to gather this data, and we are working with partners to make this crucial data freely available and keep it up-to-date. Hosted on the AWS cloud, we have seeded our curated data lake with COVID-19 case tracking data from Johns Hopkins and The New York Times, hospital bed availability from Definitive Healthcare, and over 45,000 research articles about COVID-19 and related coronaviruses from the Allen Institute for AI.

The COVID-19 dashboard includes data on city/town COVID-19 activity, confirmed and probable cases of COVID-19, confirmed and probable deaths related to COVID-19, and the demographic characteristics of cases and deaths.

Data collected by the European Centre for Disease Prevention and Control. The downloadable data file is updated daily and contains the latest available public data on COVID-19. Public-use data files allows users to manipulate the data in a format appropriate for their analyses. Users of ECDC public-use data files must comply with data use restrictions to ensure that the information will be used solely for statistical analysis or reporting purposes. For further information, visit https://www.ecdc.europa.eu/en/novel-coronavirus-china.

Note: This dataset is no longer being updated as of September 20, 2025.

The dashboard is updated each Friday.

Laboratory surveillance data: California laboratories report SARS-CoV-2 test results to CDPH through electronic laboratory reporting. Los Angeles County SARS-CoV-2 lab data has a 7-day reporting lag. Test positivity is calculated using SARS-CoV-2 lab tests that has a specimen collection date reported during a given week. Specimens for testing are collected from patients in healthcare settings and do not reflect all testing for COVID-19 in California. Test positivity for a given week is calculated by dividing the number of positive COVID-19 results by the total number of specimens tested for that virus. Weekly laboratory surveillance data are defined as Sunday through Saturday.

Hospitalization data: Data on COVID-19 and influenza hospital admissions are from Centers for Disease Control and Prevention’s (CDC) National Healthcare Safety Network (NHSN) Hospitalization dataset. The requirement to report COVID-19-associated hospitalizations was effective November 1, 2024. CDPH pulls NHSN data from the CDC on the Wednesday prior to the publication of the report. Results may differ depending on which day data are pulled. Admission rates are calculated using population estimates from the P-3: Complete State and County Projections Dataset (https://dof.ca.gov/forecasting/demographics/projections/) provided by the State of California Department of Finance. Reported weekly admission rates for the entire season use the population estimates for the year the season started. For more information on NHSN data including the protocol and data collection information, see the CDC NHSN webpage (https://www.cdc.gov/nhsn/index.html). Weekly hospitalization data are defined as Sunday through Saturday.

Death certificate data: CDPH receives weekly year-to-date dynamic data on deaths occurring in California from the CDPH Center for Health Statistics and Informatics. These data are limited to deaths occurring among California residents and are analyzed to identify COVID-19-coded deaths. These deaths are not necessarily laboratory-confirmed and are an underestimate of all COVID-19-associated deaths in California. Weekly death data are defined as Sunday through Saturday.

Since the spread of the coronavirus (COVID-19) in Italy, started in February 2020, many people who contracted the infection died. The number of deaths amounted to 198,683 as of January 8, 2025. On December 3, 2020, 993 patients died, the highest daily toll since the start of the pandemic. The region with the highest number of deaths was Lombardy, which is also the region that registered the highest number of coronavirus cases. Italy's death toll was one of the most tragic in the world. In the last months, however, the country saw the end to this terrible situation: as of November 2023, roughly 85 percent of the total Italian population was fully vaccinated. For further information about the coronavirus (COVID-19) pandemic, please visit our dedicated Facts and Figures page.

Data on COVID-19 (coronavirus) by Our World in Data

Our complete COVID-19 dataset is a collection of the COVID-19 data maintained by Our World in Data. It is updated daily and includes data on confirmed cases, deaths, and testing, as well as other variables of potential interest.

🗂️ Download our complete COVID-19 dataset : CSV | XLSX | JSON

We will continue to publish up-to-date data on confirmed cases, deaths, and testing, throughout the duration of the COVID-19 pandemic.

Our data sources

• Confirmed cases and deaths: our data comes from the European Centre for Disease Prevention and Control (ECDC). We discuss how and when the ECDC collects and publishes this data here. The cases & deaths dataset is updated daily. *Note: the number of cases or deaths reported by any institution—including the ECDC, the WHO, Johns Hopkins and others—on a given day does not necessarily represent the actual number on that date. This is because of the long reporting chain that exists between a new case/death and its inclusion in statistics. This also means that negative values in cases and deaths can sometimes appear when a country sends a correction to the ECDC, because it had previously overestimated the number of cases/deaths. Alternatively, large changes can sometimes (although rarely) be made to a country's entire time series if the ECDC decides (and has access to the necessary data) to correct values retrospectively.*
• Testing for COVID-19: this data is collected by the Our World in Data team from official reports; you can find further details in our post on COVID-19 testing, including our checklist of questions to understand testing data, information on geographical and temporal coverage, and detailed country-by-country source information. The testing dataset is updated around twice a week.
• Other variables: this data is collected from a variety of sources (United Nations, World Bank, Global Burden of Disease, Blavatnik School of Government, etc.). More information is available in our codebook.

The complete Our World in Data COVID-19 dataset

Our complete COVID-19 dataset is available in CSV, XLSX, and JSON formats, and includes all of our historical data on the pandemic up to the date of publication.

The CSV and XLSX files follow a format of 1 row per location and date. The JSON version is split by country ISO code, with static variables and an array of daily records.

The variables represent all of our main data related to confirmed cases, deaths, and testing, as well as other variables of potential interest.

As of 10 September 2020, the columns are: iso_code, continent, location, date, total_cases, new_cases, new_cases_smoothed, total_deaths, new_deaths, new_deaths_smoothed, total_cases_per_million, new_cases_per_million, new_cases_smoothed_per_million, total_deaths_per_million, new_deaths_per_million, new_deaths_smoothed_per_million, total_tests, new_tests, new_tests_smoothed, total_tests_per_thousand, new_tests_per_thousand, new_tests_smoothed_per_thousand, tests_per_case, positive_rate, tests_units, stringency_index, population, population_density, median_age, aged_65_older, aged_70_older, gdp_per_capita, extreme_poverty, cardiovasc_death_rate, diabetes_prevalence, female_smokers, male_smokers, handwashing_facilities, hospital_beds_per_thousand, life_expectancy, human_development_index

A full codebook is made available, with a description and source for each variable in the dataset.

Additional files and information

If you are interested in the individual files that make up the complete dataset, or more detailed information, other files can be found in the subfolders:

• ecdc: data fro...

Full-text and metadata dataset of COVID-19 and coronavirus-related research articles optimized for machine readability.

Rates per 100,000 population Click on the buttons below to see data for the different metrics:

Cases

Deaths

By Income
By Region

COVID Data for Shared Learning (CDSL) is a multimodal database comprising de-identified medical data from 4,479 patients who were hospitalized with confirmed or suspected COVID-19 in the Spanish 'HM Hospitales' group from 2019-12-26 to 2021-02-13. The database provides tabular demographic, diagnostic, clinical and treatment information, as well as radiological images in JPG format, namely chest X-ray and computed tomography scans. The primary goal of CDSL is to develop a comprehensive toolkit to support researchers and institutions in building multimodal models for prediction, classification and optimization. CDSL database was promptly shared with the international research community at the onset of the COVID-19 pandemic to promote worldwide collaboration and, ultimately, guide policy decisions and facilitate effective response efforts studies on the disease.

CLUSTREC-COVID: A Topical Clustering Benchmark for COVID-19 Scientific Research

  Dataset Summary

CLUSTREC-COVID is a modified version of the TREC-COVID dataset, transformed into a topical clustering benchmark. The dataset consists of titles and abstracts from scientific papers about COVID-19 research, covering a diverse range of research topics. Each document in the dataset is assigned to a specific subtopic, making it ideal for use in document clustering and topic… See the full description on the dataset page: https://huggingface.co/datasets/Uri-ka/ClusTREC-Covid.

After over two years of public reporting, the State Profile Report will no longer be produced and distributed after February 2023. The final release was on February 23, 2023. We want to thank everyone who contributed to the design, production, and review of this report and we hope that it provided insight into the data trends throughout the COVID-19 pandemic. Data about COVID-19 will continue to be updated at CDC’s COVID Data Tracker.

The State Profile Report (SPR) is generated by the Data Strategy and Execution Workgroup in the Joint Coordination Cell, in collaboration with the White House. It is managed by an interagency team with representatives from multiple agencies and offices (including the United States Department of Health and Human Services (HHS), the Centers for Disease Control and Prevention, the HHS Assistant Secretary for Preparedness and Response, and the Indian Health Service). The SPR provides easily interpretable information on key indicators for each state, down to the county level.

It is a weekly snapshot in time that:

• Focuses on recent outcomes in the last seven days and changes relative to the month prior
• Provides additional contextual information at the county level for each state, and includes national level information
• Supports rapid visual interpretation of results with color thresholds